% This is ntbpub.bib file

%ngroup.bib and ntbpub.bib are our two .bib files
%customized fields are nremark, nlocation, nack, nabstract
%Additions and corrections in .bib  format can be emailed to meiqing
%who will periodically update the file.
%
%The scope of ngroup.bib
%is computational methods for biomolec modeling
%ranging from cs issues like vectorization thru na to amtp issues like
%Fixman potentials. Also it is to include general references of relevance
%in computing, math, science, and technical writing.
%The scope of ntbpub.bib is our publications supported by grants here.


@article{Skee91,
        author = {R. D. Skeel},
        title = "Macromolecular dynamics on a shared-memory multiprocessor",
         journal =  "J. Comput. Chem. ",
volume=12,
        year = "1991",
nremark = "also, Rpt. No. 929, Center for Supercomputing Research
and Development, Univ. of Illinois, Urbana, 1989"
}

@techreport{HoSa92a,
author = {M.~Holst and F.~Saied},
number = {UIUCDCS-R-92-1744},
year = 1992,
nack = {doe}
}

@techreport{Okun92a,
author="D.~Okunbor",
title="Canonical Numerical Integrators for {H}amiltonian Dynamical
 Systems",
number="UIUCDCS-R-92-1785",
 institution="Dept. of Computer Sci., Univ. of Illinois at Urbana-Champaign,
 Urbana, Illinois, USA", year=1992,
note="(Ph.D. Thesis)"
}

@article{Okun92b,
author = {D. Okunbor},
title = "Canonical Methods for {H}amiltonian Systems:
 Numerical Experiments",
    journal = "Physica D",
    volume = 60,
    year = 1992,
    pages = "314-322"
}

@article{OkSk92a,
        author = {D. Okunbor and R. D. Skeel},
        title = "An explicit Runge-Kutta-Nystrom method is canonical if and only
 if its adjoint is explicit",
        journal = "SIAM J. Numer. Anal. ",
       volume=  29,
   pages=" 521-527",
        year = "1992"
}

@article{OkSk92b,
        author = {D. Okunbor and R. D. Skeel},
        title = "Explicit canonical methods for {H}amiltonian systems",
         journal =  "Math. Comput.",
        volume= 59, pages="439-455",
month= oct, number= 200,
        year = "1992"
}

@article{SkGe92,
        author = {R. D. Skeel and C. W. Gear},
        title = "Does variable step size ruin a symplectic integrator?",
         journal =  "Physica D ",
      volume=60, pages="311-313",
        year = "1992",
        address = ""
}

@article{BiSk93,
        author = {J. J. Biesiadecki and R. D. Skeel},
        title = "Dangers of Multiple-Time-Step Methods",
        journal = "J. Comput. Phys.",
        volume= 109, number = 2, pages="318--328",
  nack =    "NSF90, NIH92",
        year = "1993", month = dec,
nremark={ symplectic MTS(Verlet I) and Verlet X}
}

@phdthesis{Hols93,
author = {M. Holst},
title = {Multigrid Solution of the {P}oisson--{B}oltzmann Equation},
year = 1993,
school = {Dept.\ of Computer Science, 
 Univ.\ of Illinois at Urbana--Champaign},
nack = {doe}
}

@article{HoSa93a,
author = {M.~Holst and F.~Saied},
journal = {J.~Comp.~Chem.},
volume = 14,
year =1993,
pages = {105--113},
nack = {doe}
}

@article{Okun93,
        author = {D. Okunbor},
 title = "Variable step size does not harm second-order
 integrators for {H}amiltonian systems",
        journal = "J. Comput.\ Appl.\ Math.",
       volume=  47, number = {2},
   pages="273--279", 
nremark= {"% doubt about whether 273 is a page number",
   "Letter"},
        year = "1993"
}

@article{Skee93,
        author = {R. D. Skeel},
 title
= "Variable Step Size Destabilizes the {S}t{\"o}rmer/Leapfrog/{Verlet} Method",
         journal =  "BIT", volume= 33, pages="172-175",
        year = "1993",
        address = ""
}

@inproceedings{SkBO93,
        author = {R. D. Skeel and J. Biesiadecki and D. Okunbor},
        title = "Symplectic integration for macromolecular dynamics",
         booktitle =  "Proceedings of the International Conference on
 Computation of Differential Equations and Dynamical Systems",
editor = {Kang Feng and Zhong-Ci Shi},
nremark = {Beijing P. R. China, September 1--5},
    publisher="World Scientific Publishing Co.",
    pages="49-61", nack = "NSF90",
        year = "1993",
        address = "Singapore"
}

@book{SkKe93,
author = {Robert D. Skeel and Jerry B. Keiper},
title = {Elementary Numerical Computing with Mathematica},
publisher = {McGraw-Hill},
address = {New York},
year = 1993
}
		  
@article{BKSS94,
        author = "John A. Board Jr. and Laxmikant V. Kal\'e and
        Klaus Schulten and Robert D. Skeel and Tamar Schlick",
        title = "Modeling Biomolecules: Larger Scales, Longer Durations",
        journal = "IEEE Computational Science \& Engineering",
        volume= 1, pages="19--30",
        nack = "NSF/ARPA93",
        year = "1994",
        month = "Winter",
       ack={GC}
}

@article{HKSS94a,
author = {M. Holst and R.~E.~Kozack and F.~Saied and S.~Subramaniam},
title = {Protein Electrostatics:  Rapid Multigrid-based {N}ewton
Algorithm for Solution of the Full Nonlinear {P}oisson--{B}oltzmann Equation},
journal = {J. Biomol.\ Struct.\ Dyn.},
volume = 11, number = 6,
pages = {1437--1445},
year = 1994,
nack = {presumably this is the paper submitted to Nature that acks DOE}
}

@article{HKSS94b,
   author    = "M. Holst and R. Kozack and F. Saied and S. Subramaniam",
   title     = "Treatment of electrostatic effects in proteins: 
                {M}ultigrid-based {N}ewton iterative method for solution 
                of the full nonlinear {Poisson--Boltzmann} equation",
   journal   = "{P}roteins: {S}tructure, {F}unction, and {G}enetics",
   volume    = "18",
   pages     = "231--245",
   number    = "3",
   year      = 1994,
remark = {[Beckman Institute Technical Report UIUC-BI-MB-93-01]},
nlocation ="in BI files?"
}

@article{LeSk94,
        author = {B. Leimkuhler and R. D. Skeel},
title = "Symplectic numerical integrators
 in constrained {H}amiltonian systems",
        journal = "J. Comput. Phys.",
  volume= 112, pages="117-125", Number= 1, month="May",
 nack = "NSF90",
        year = "1994",
        address = ""
}

@article{OkSk94a,
        author = {D. Okunbor and R. D. Skeel},
    title = "Canonical numerical methods for molecular dynamics simulations",
         journal =  "J. Comput. Chem.",
 volume= 15, pages="72-79",
 number= 1,  month= jan,
 nack = "NSF90, NIH92",
        year = "1994",
        address = ""
}

@article{OkSk94b,
        author = {D. Okunbor and R. D. Skeel},
        title = "Canonical Runge-Kutta-Nystrom methods of orders 5 and 6",
         journal =  "J. Comp. Appl. Math.",
         volume="51",
        year = "1994",
pages = {375--382}
}

@article{SkBi94,
        author = {R. D. Skeel and J. J. Biesiadecki},
        title = "Symplectic integration with variable stepsize",
         journal =  "Annals of Numer. Math. ",
        volume=1, pages="191-198", nack = "NSF90, NIH92",
        year = "1994",
	nremark = {introduces artificial splittings}
}

@article{BKLS95,
    author = {E. Barth and K. Kuczera  and B. Leimkuhler and R. D. Skeel},
    title = "Algorithms for Constrained Molecular Dynamics",
    journal = "J. Comput.\ Chem. ",
    nack = "NIH, DOE/NSF93",
    year = "1995",
    month = oct,
    volume = 16,
    number = 10,
    pages = {1192--1209}
}

@article{NHGD95a,
author="Mark Nelson and William Humphrey and Attila Gursoy and  Andrew Dalke
 and Laxmikant Kal\'e and Robert Skeel and Klaus Schulten and  Richard Kufrin",
 title="{MDScope}---A Visual Computing Environment for Structural Biology", 
journal={Comput.\ Phys.\ Commun.}, 
year=1995,
pages = {111--134},
month = oct # {~14,},
volume = 91,
number = {1, 2 and 3},
nremark={[Beckman Institute Technical Report TB-94-18]},
 ack = {NIH, GC}
}

@inproceedings{NHGD95b,
  author={Mark Nelson and William Humphrey and Attila Gursoy and Andrew Dalke
  and Laxmikant Kal\'e and Robert Skeel and Klaus Schulten and Richard Kufrin},
  title={{MDScope}---A Visual Computing Environment for Structural  
Biology},
  booktitle={{ICES '95} Conference Proceedings---Computational Mechanics 95},
editor = {S.N. Atluri and G. Yagawa and T.A. Cruse},
  volume = 1,
  year=1995,
pages ={476--481},
  nremark={a shortened version of the CPC paper for
a conference, organized by A. Sameh and others, that KS is invited to.
It is a 6 page version of
the CPC paper, all text taken straight from the CPC paper, with no 
figures.}
}

@article{Reic95,
author = {Sebastian Reich},
title = {Smoothed Dynamics of Highly Oscillatory {H}amiltonian Systems},
nremark =  {also Reich, S., Molecular dynamics with soft constraints,
Technical Report UIUC-BI-TB-94-12, Beckman Institute, Urbana, 1994.},
year = 1995,
journal = {Physica D},
month = dec # {~21,},
volume = 89,
number = {1 and ~2},
pages = {28--42},
nack = {doe/nsf, nsf/arpa gcag, nih}
}

@article{Skee95,
title = { Numerical {H}amiltonian {P}roblems
 ({J}. {M}. {S}anz-{S}erna and {M}. {P}. {C}alvo)},
author = {Robert D. Skeel},
journal = {SIAM Review},
pages = {},
year = 1995,
month = {June},
volume = {37},
issue = {2}
}

@unpublished{Zhan95,
author = {Meiqing Zhang},
title = {Stabilization of the {S}t\"ormer/{V}erlet Method},
note = {Manuscript},
year = 1995,
month = {July 28,}
}

@article{ZhSk95,
        author = {M. Q. Zhang and R. D. Skeel},
      title="Symplectic Integrators and the Conservation of Angular Momentum",
         journal =  "J. Comput. Chem. ",
volume="16" , month= mar,
 nack = "NIH, DOE/NSF93, GC",
        year = "1995",
         pages=" 365--369",
nremark = {542.805 JO},
nlocation = {CHX}
}

@incollection{LeRS96,
   author = {Benedict J. Leimkuhler and Sebastian Reich and Robert D. Skeel},
        title = "Integration methods for molecular dynamics",
 booktitle =  "Mathematical Approaches to Biomolecular Structure and Dynamics",
    publisher="Springer-Verlag",
    pages="161--185",
   editor={Jill P. Mesirov and Klaus Schulten and De Witt Sumners},
        year = "1996",
nack = {NSF/DOE, NSF/ARPA, NIH},
series = {IMA Volumes in Mathematics and its Applications},
volume = 82
}

@article{Reic96,
author = {Sebastian Reich},
title = {Enhancing Energy Conserving Methods},
journal = {BIT Numer.\ Math.},
year = 1996,
number = 1, volume = 36,
pages = {122--134},
nack = {doe/nsf, nsf/arpa gcag, nih}
}
     
@inproceedings{LoSS96a,
        author = "M. L\'opez-Marcos and J. M. Sanz-Serna and R. D. Skeel",
        title = "Cheap Enhancement of Symplectic Integrators",
booktitle =  "Numerical Analysis 1995",
    publisher="Longman Group",
address = {London},
    pages="107-122",
   editor={D. F. Griffiths and G. A. Watson},
year = 1996,
nack = {Iber, doensf, nsfarpa, nih},
nrights = {to include in other volumes of our own work}
}
   
@incollection{LoSS96b,
        author = "M. L\'opez-Marcos and J. M. Sanz-Serna and R. D. Skeel",
booktitle = {Numerical Analysis, {A}. {R}. {M}itchell 75th Birthday Volume},
editor = {D. F. Griffiths and G. A. Watson},
publisher = {World Scientific},
nremark = {ISBN:       981-02-2719-1},
address = {Singapore},
year = 1996, month = {June},
pages = "163--176",
title = "Explicit Symplectic Integrators with Maximal Stability Intervals",
nack = {Iber, doensf, nsfarpa, nih}
}

@article{NHGD96,
  author={Mark Nelson and William Humphrey and Attila Gursoy and Andrew Dalke
  and Laxmikant Kal\'e and Robert D. Skeel and Klaus Schulten},
  title={{NAMD}---a Parallel, Object-Oriented Molecular Dynamics Program},
  journal={Intl.\ J. Supercomput.\ Applics.\ High Performance Computing},
year = 1996,
month = {Winter},
volume = 10, number = 4,
pages = {251--268},
  nremark={[Beckman Institute Technical Report TB-95-17]}
}
    
@article{LoSS97,
        author = "M. L\'opez-Marcos and J. M. Sanz-Serna and R. D. Skeel",
    title = "Explicit Symplectic Integrators Using {H}essian--Vector Products",
    pages="223-238",
journal = {SIAM J. Sci. Comput.},
volume = {18},
year = {1997},
month = jan,
nack = {Iber, doensf, nsfarpa, nih}
}

@article{SkZS97,
title = {A family of symplectic integrators: stability, accuracy, and
molecular dynamics applications},
author = {Robert D. Skeel and Guihua Zhang and Tamar Schlick},
pages="203-222",
journal = {SIAM J. Sci. Comput.},
volume = 18,
number = 1,
year = 1997,
month = jan,
ack = {doe91, nsf93, gc, nih92}
}

@article{LiSZ97,
title={Error Analysis of Symplectic Multiple Time Stepping},
author={Todd R. Littell and Robert D. Skeel and Meiqing Zhang},
journal = {SIAM J. Numer.\ Anal.},
year = 1997,
month  = oct,
volume = 34,
number = 5,
pages = {1792--1807},
nack={NIH92,  NSF/ARPA93 and by DOE/NSF93, Iber.}
}

@article{BiSS97,
  author = "T. Bishop and Robert D. Skeel and K. Schulten",
  title = "Difficulties with Multiple Timestepping and
the Fast Multipole Algorithm in Molecular Dynamics",
    pages="1785--1791",
journal = {J. Comput.\ Chem.},
volume = {18}, number = 14,
year = {1997},
month = nov # {~15,},
nack = {nsf96, nsfgc, nih}
}

@article{ZhSk97,
title = {Cheap Implicit Symplectic Integrators},
author = {Meiqing Zhang and Robert D. Skeel},
volume = 25,
year = 1997,
pages = {297--302},
journal = {Appl.\ Num.\ Math.}
}

@inproceedings{GaSS98,
 author = "B. Garc\'{\i}a-Archilla and J. M. Sanz-Serna and Robert D. Skeel",
title = {The Mollified Impulse Method for Oscillatory Differential Equations},
booktitle =  "Numerical Analysis 1997",
publisher = "Pitman",
address = {London},
    pages="111--123",
   editor={D. F. Griffiths and G. A. Watson},
year = 1998,
nremark = {[Also, Rept.\ No.\ 1997/5, Dept.\ Mat.\ Aplic.\ Comput.,
Univ.\ de Valladolid, Spain, July 1997.]},
nack = {Iber, nsf96, nsfarpa, nih},
nrights = {to include in other volumes of our own work}
}

@article{SMSS98,
author = {Tamar Schlick and Margaret Mandziuk and
Robert D. Skeel and K. Srinivas},
title = {Nonlinear Resonance Artifacts in Molecular Dynamics Simulations},
journal = {J. Comput.\ Phys.},
volume = 139,
year = 1998,
pages = {1--29},
nack = {nsf96, nih, nsf/arpa}
}

@book{DHLM98, 
title = {Computational Molecular Dynamics: Challenges, Methods, Ideas},
editor = {P. Deuflhard and J. Hermans and B. Leimkuhler and A. Mark and
 S. Reich and R.~D. Skeel},
series = {Lecture Notes in Computational Science and Engineering},
volume = 4,
publisher = {Springer-Verlag},
year = 1998, month = nov,
nremark = {89 pp. ISBN 3-540-63242-5 Softcover DM 149,-
ISBN 3-540-63242-5       DM 149,00/US $ 89,00    XI, 489 pp

"On May 21-24, 1997 the Second International Symposium on Algorithms for
Macromolecular Modelling was held at the Konrad-Zuse-Zentrum in Berlin.
The event brought together computational scientists in fields like
biochemistry, biophysics, physical chemistry, or statistical physics and
numerical analysts as well as computer scientists working on the
advancement of algorithms, for a total of over 120 participants from 19
countries. In the course of the symposium, the speakers agreed to
produce some representative volume that combines survey articles and
original papers (all refereed) to give an impression of the present
state of the art of Molecular Dynamics. The 29 articles of the book
reflect the main topics of the Berlin meeting which were i)
Conformational Dynamics, ii) Thermodynamic Modelling, iii) Advanced
Time-Stepping Algorithms, iv) Quantum-Classical Simulations and Fast
Force Field and v) Fast Force Field Evaluation."
}
}

@incollection{SkIz98, 
author={Robert D. Skeel and Jes\'us Izaguirre}, 
title = {The Five Femtosecond Time Step Barrier},
booktitle = {Computational Molecular Dynamics: Challenges, Methods, Ideas},
editor = {P. Deuflhard and J. Hermans and B. Leimkuhler and A. Mark and
S. Reich and R.~D. Skeel},
series = {Lecture Notes in Computational Science and Engineering},
volume = 4,
publisher = {Springer-Verlag},
pages = {303--318},
year = 1998, month = nov,
nack = {This work was supported in part by NIH Grant P41RR05969 and
NSF Grants BIR-9318159 and DMS-9600088.}
}

@incollection{PBSB98, 
author={James C.~Phillips and Robert Brunner and  
Aritomo Shinozaki and Milind Bhandarkar and Neal Krawetz and  
Attila Gursoy and Laxmikant Kal\'e and Robert D.~Skeel and Klaus Schulten},
title
 = {Avoiding Algorithmic Obfuscation in a Message-Driven Parallel {MD} Code},
booktitle = {Computational Molecular Dynamics: Challenges, Methods, Ideas},
editor = {P. Deuflhard and J. Hermans and B. Leimkuhler and A. Mark and
 S. Reich and R.~D. Skeel},
series = {Lecture Notes in Computational Science and Engineering},
volume = 4,
publisher = {Springer-Verlag},
pages = {455-468},
year = 1998, month = nov,
nack = {This work was supported in part by NIH Grant P41RR05969 and
NSF Grants BIR-9318159.}
}
    
@article{GaSS98,
 author = "B. Garc\'{\i}a-Archilla and J. M. Sanz-Serna and Robert D. Skeel",
    title = "Long-Time-Step Methods for Oscillatory Differential Equations",
nremark = {To appear.  {[Also Tech. Rept. 1996/7,
Dep.\ Math.\ Aplic.\ Comput., Univ. Valladolid, Valladolid, Spain]}
Available by anonymous ftp from ftp.mac.cie.uva.es
 as /pub/reports/Report96_7.ps
pdf, ps, ps.Z, dvi available from
http://epubs.siam.org/sam-bin/dbq/article/31385
},
journal = {SIAM J. Sci.\ Comput.},
volume = {20}, number = 3,
year = {1998},
month = oct # {~20,},
pages = {930--963},
nack = {Iber, nsf96, nsfarpa, nih}
}
		  
@article{Skee98,
author = "Robert D. Skeel",
        title = "Comments on `{N}umerical Instability due to Varying Time
Steps in Explicit Wave Propagation and Mechanics Calculations'
by {J}oseph~{P}. {W}right",
 journal = "J. Comput.\ Phys.",
        volume= "145", pages="758--759",
        year = "1998"
}

@article{Skee99a, 
author={Robert D. Skeel}, 
title={Symplectic Integration with Floating-Point Arithmetic
and Other Approximations},
pages = {3--18},
volume = 29,
nremark = {Available by anonymous ftp from ftp.cs.uiuc.edu
 as /pub/faculty/skeel/Preprints/Skee9y.ps,
 PDF at http://www.elsevier.nl/locate/apnum},
journal={Appl.\ Numer.\ Math.},
year={1999},
nack={ NSF Grant DMS-9600088, 
NSF Grant BIR-9318159, and NIH Grant P41RR05969.}
}

@article{HaOS99, 
author={D. J. Hardy and D. I. Okunbor and R. D. Skeel}, 
title={Symplectic Variable Stepsize Integration for {$N$}-Body Problems}, 
nremark = {
Available by anonymous ftp from ftp.cs.uiuc.edu
 as /pub/faculty/skeel/Preprints/HaOS9y.ps,
 PDF at http://www.elsevier.nl/locate/apnum
},
journal={Appl.\ Numer.\ Math.},
volume = 29,
year={1999},
pages = {19--30},
nack={Work by first and second authors supported in part by 
NSF Grant CCR-9408973; work by first and third authors supported 
in part by NSF Grant DMS-9600088, 
NSF Grant BIR-9318159, and NIH Grant P41RR05969.}
}
		  
@article{SSBK99,
author = "Tamar Schlick and Robert D. Skeel  and Axel T. Br{\"u}nger
 and Laxmikant V. Kal\'e and John A. {Board, Jr.} and Jan Hermans 
 and Klaus Schulten",
 title = "Algorithmic Challenges in Computational Molecular Biophysics",
 journal = "J. Comput.\ Phys.",
pages = {9--48}, volume = 151, number = 1,
nremark = {Special issue},
        nack = "NSF93",
        year = 1999,
        month = may # {,~1}
}
		  
		  
@article{KSBB99,
author = {L. Kal\'e and R. Skeel and R. Brunner
 and M. Bhandarkar and  A. Gursoy and N. Krawetz and J. Phillips and  
A. Shinozaki and K. Varadarajan and K. Schulten},
 title = {{NAMD2}:  Greater Scalability for Parallel Molecular Dynamics},
pages = {283--312},
journal = {J. Comput.\ Phys}, volume = 151, number = 1,
month = may # "~1,", year = 1999,
        nack = "NSF93,NIH"
}

@incollection{Skee99b, 
author={Robert D.~Skeel},
title = {Integration Schemes for Molecular Dynamics and Related Applications},
booktitle = {The Graduate Student's Guide to Numerical Analysis},
editor = {M.~Ainsworth and J.~Levesley and M.~Marletta},
series = {SSCM},
publisher = {Springer-Verlag},
pages = {},
year = {1999},
nack = {This
work was supported in part by NSF Grant DMS-9600088,
NSF Grant BIR-9318159, and NIH Grant P41RR05969.},
note = {To appear}
}

@article{IzRS99, 
author={Jes\'us Izaguirre and Sebastian Reich and Robert D. Skeel}, 
title={Longer Time Steps for Molecular Dynamics},
journal = {J. Chem.\ Phys.}, volume = 110, number = 19,
pages = {9853--9864}, month = may # {~15,},
year = 1999,
nremark = {Available by anonymous ftp from ftp.cs.uiuc.edu
 as /pub/faculty/skeel/Preprints/IzRS9y.ps},
nack = {nih97, gcag93, nsf96}
}

@unpublished{SkSr9x,
	author = "{R. D. Skeel and K. Srinivas}",
	title = "Nonlinear Stability Analysis of Area-Preserving Integrators",
	 journal =  "SIAM J. Numer.\ Anal.",
        volume="", pages="",
note = {To appear pending major revision},
	year = "199x",
	address = ""
}

@misc(EndOfFile,
 title=" ",
 author=" ",
 comment="this is end of file only for my transform .bib file to .tex's
 c-program use",
)

